Conserved energy for v-rescale thermostat drifts

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GROMACS version: 2019.4, 2020.6
GROMACS modification: No

Hello,

I was running NVT equilibrations for a small protein (about 100 residues) in TIP3P water (about 30,000 atoms in total) using the v-rescale thermostat (varying tau_t) with standard simulation parameters and the AMBER99SB-ildn force field as provided in GROMACS:

integrator = md
nsteps = 200000
dt = 0.001

constraints = h_bonds

cutoff_scheme = verlet
coulombtype = PME
fourierspacing = 0.12
pme_order = 6

tcoupl = v_rescale
tc_grps = Protein non-Protein
tau_t = 0.1 0.1
ref_t = 300 300

gen_vel = yes
gen_temp = 300
continuation = no

Before the equilibration, the system was well minimised (first steepest decent, then conjugate gradient up to the single-precision limit).

Now, when I check the temperature evolution, everything seems fine (see figure below).

But when I look at the “Conserved Energy” quantity written to the EDR file (which as I understand refers to the conserved quantity for the thermostat as described here: J. Chem. Phys. 126, 014101 (2007); https://doi.org/10.1063/1.2408420), it shows an apparent drift. The absolute drift has a small scale but compared to the fluctuation of this quantity it still seems substantial.

My questions are: Should I worry about this? If yes, what could potentially cause this?

I already tested with “DispCorr = No” (as I guess is recommended for the force field) and “DispCorr = EnerPress” (not shown) but the trend is the same.

nvt_sanity
nvt_sanity1754Ă—1084 135 KB

2

Numerical integration never perfectly conserves energy. This drift is very small, so nothing to worry about.
The largest sources of drift are usually the constraint algorithm(s), which always give a negative drift, and the errors allowed by the verlet-buffer-tolerance parameter, which usually give a positive drift.

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